Prerna Bansal

20 Questions 14 Answers 0 Followers

Questions related from Prerna Bansal

Can we draw a cylindrical shape using PACKMOL?

I want to make a cylindrical shape configuration for my study using PACKMOL, can anybody suggest what would be the input file change in it if we use sphere for spherical shape. i tried replacing...

03 March 2019 5,510 2 View

In GROMACS, how to nvt equilibrate without restraints after NPT simulation with restsraints?

Hi,I am trying to NVT equilibrate without constraints after NPT simulation with constraints. but i am getting the errors in tau_t and many more. can anyone suggest what is wrong with the mdp file.

03 March 2019 7,829 5 View

In VMD, inorganic builder, hw can i build a device for a given unit cell?

while giving new material option and browse unit cell, it asked for topology file which i tried to generate using GROMACS but when i upload it and try to build device, it says non-invertible...

02 February 2019 2,141 1 View

HI everyone, i am getting fatal error in GROMACS as no residue type for MET. could anyone help?

Fatal error: In the chosen force field there is no residue type for 'MET' as a standalone (starting & ending) residue

02 February 2019 7,112 3 View

Cannot find position restraint file restraint.gro (option -r)?

Hello everyone, while running nvt equilibration i am getting the error as: Cannot find position restraint file restraint.gro (option -r). From GROMACS-2018, you need to specify the position...

02 February 2019 9,790 1 View

Fatal error:unable to open extended system file, NAMD?

i am getting this error while running NAMD could anyone help...

01 January 2019 8,139 3 View

Charm++ Fatal error while running NAMD?

Hi Everyone, I am trying to run the NAMD configuration file but as soon as i run the command as namd2 minimize.namd > dummy.out it gives an error as: charm++ fatal error: unable to...

01 January 2019 1,738 8 View

Fatal error: Can not read file ions.tpr, this file is from a GROMACS version which is older than 2.0 Make a new one with grompp?

Fatal error: Can not read file ions.tpr, this file is from a GROMACS version which is older than 2.0 Make a new one with grompp or use a gro or pdb file, if possible can...

10 October 2018 7,204 2 View

Transition state doesn't seem to converge in Gaussian using QST2 although its chk point file shows the vibration for bond which would break?

does that mean reaction proceeds via SN1 mechanism or the TS doesn't exists?

08 August 2018 5,885 1 View

Is there any way to check if any transition state would exist for a reaction in Gaussian if the QST2 run fails or the reaction is diffusion controll?

Gaussian

07 July 2018 7,520 0 View

How do i eliminate this error in gromacs while running pdb2gmx commandFatal error: Atom HB3 in residue ASP 144 was not found in rtp entry NASP with ?

Gromacs

06 June 2018 10,194 4 View

Can we use a protein having more than one docked ligand for protein ligand simulations in GROMACS?

GROMACS

06 June 2018 2,985 1 View

Can anyone help?This is likely either a 1,4 interaction, or a listed interc inside asmaller mol you are decoupling during a free energy calc?

Gromacs

06 June 2018 10,002 0 View

What are the best software for treating nanoparticles apart from materials suite-schrodinger?

09 September 2016 6,026 4 View

Is it correct to perform homology modelling of a particular length of fasta sequence rather complete fasta sequence?

is it correct to perform homolgy modelling of a particular length of fasta sequence rather complete fasta sequence?

03 March 2015 6,716 5 View

What is the possible reason for the error writwa in gaussian inspite of the fact that the system has large amount of hard disk and great RAM?

Gaussian

10 October 2014 8,394 0 View

I can't create file Temp input file 'GXX.INP. What will the solution to this error be in gaussian?

gaussian

06 June 2014 4,392 3 View

While using CIS in gaussian we calculate various possible excited states, but how is it possible to optimise a particular state of interest?

02 February 2014 8,814 0 View

How do we decide whether tunneling is one dimensional or multidimensional for a given reaction?

Quantum tunneling

10 October 2013 8,275 1 View

Can gaussian 09 also display hydrogen bonding?

Gaussian

04 April 2013 7,399 7 View